Always always always in any transaction where you are the buyer, remember the money is in your pocket (or account or custody of some sort) and you are in complete control. Do not hesitate to say repeatedly "well that would be a deal breaker. I can't have that." and see how fast they change their tactics.
With Dell for example, I'm sure that deal is water under the bridge and I'm not trying to critique anyone, but if you do a deal with them again and they're on the phone with you, don't hesitate to say not only does the $50 charge not work but you should get a $150 credit or no deal, and see where/ if they meet you in the middle somewhere.
There is tremendous margin in those systems. I paid $1200 for a QX6850 that I would guess michael dell gets for around $250 or so because he buys them by the trainload and does his own warranty. He may even pay less. Plus with the add-ons they mark them up 500% or more and don't credit for the base parts you're not getting.
If you know the seller's margins, strengths/ weaknesses, etc. you have leverage. Don't hesitate to walk from a deal. There's always someone willing to take your money; that will never change.